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5 July begins as a normal winter morning near Hamilton, New Zealand. At 6:12 a.m., the Sun darkens for a moment, and a red light surrounded by darkness is briefly seen.

Zac Hobson (Bruno Lawrence) is a scientist working for Delenco, part of an international consortium working on "Project Flashlight", an experiment to create a global energy grid. He awakens abruptly; when he turns on his radio, he is unable to receive any transmissions. Zac gets dressed and drives into the deserted city. Investigating a fire, he discovers the wreckage of a passenger jet, but there are no bodies, only empty seats.

He enters his underground laboratory; a monitor displays the message "Project Flashlight Complete". The mass disappearance seems to coincide with the moment Flashlight was activated. He notes on his tape recorder:

"Zac Hobson, July 5th. One: there has been a malfunction in Project Flashlight with devastating results. Two: it seems I am the only person left on Earth."

From this point onward, Zac refers to the crucial moment and its result as "The Effect".

After several days, his mental state begins to deteriorate. He puts on a woman's slip and alternates between exhilaration and despair. Eventually he breaks down altogether. He assembles cardboard cutouts of famous people (including Adolf Hitler, Elizabeth II, and Pope John Paul II) and addresses them from a balcony. He declares himself "President of this Quiet Earth", then goes on a rampage. He later bursts into a church and shoots a statue of Jesus off a crucifix. After accidentally crushing an empty pram, he puts the barrel of a shotgun in his mouth, but changes his mind when he witnesses an explosion resulting from his destruction.

He settles into a more normal routine. One morning, a young woman named Joanne (Alison Routledge) appears. Zac is attracted to her, and after a few days together they have sex. They decide to scour the countryside for other survivors.

They find a third survivor, a large Māori man named Api (Pete Smith). The three determine why they survived: at the instant of The Effect, they were all at the moment of death—Api was being drowned in a fight, Joanne was electrocuted by a faulty hairdryer, and Zac had overdosed on pills in a suicide attempt. He had realized there were serious dangers with the experiment and was guilt-ridden for not speaking out.

A love triangle develops, but Zac is more concerned about his observations: several universal physical constants are changing, causing the Sun's output to fluctuate. Zac fears that The Effect will occur again and decides to destroy the Delenco facility in an attempt to stop it.

The three put aside their personal conflicts and drive a truckload of explosives to the installation, only to be stopped at the perimeter when Zac detects dangerous levels of ionising radiation emanating from the plant. He says that he will go to town to retrieve a remote control device that will allow them to send the truck into the facility.

While Zac is gone, Joanne and Api have sex. Afterward, Api tells Joanne that he will sacrifice himself by driving the truck; he doubts that Zac's device will be capable of controlling the vehicle. They then hear the truck and realise that Zac did not go to town after all. He drives the truck onto the weakened roof of the underground portion of the laboratory, which collapses. Just as the effect reaches a maximum, he triggers the explosives.

Once again a red light is seen surrounded by the dark tunnel. Zac finds himself lying face down on a beach. There are strange cloud formations, resembling waterspouts, rising out of the ocean. As he walks to the water's edge, an enormous ringed planet slowly appears over the horizon. Zac stares in disbelief, then realises he is still holding his tape recorder. He lifts it up as if to speak, then lowers it, completely bewildered.

The precise meaning of the final scene is left to the audience. In his commentary on the Umbrella Entertainment DVD release, writer/producer Sam Pillsbury states, "...we all thought it was quite simple; I mean, our intention was just that, what happened was, he died at the moment of the effect for a second time and he's now found himself in another world, what the hell's he gonna do...", he then says, more or less jokingly, that director Geoff Murphy being 'a Catholic or lapsed Catholic, (it) may well have been something to do with purgatory, and y'know, you being trapped in cyclical and going back into having to relive your thing until you work out your karma, (something; possibly 'if I'm not') mixing my metaphors; anyway, enigmatic is good, I think, to a certain extent..."

^Theodore Baehr, Bruce Grimes, Lisa Ann Rice (1987), The movie & video guide for Christian families, p. 168, The Quiet Earth is a New Zealand remake of The Night of the Comet and The World, the Flesh and the Devil…